GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Desulfovibrio vulgaris Hildenborough

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate 207136 DVU1677 triosephosphate isomerase

Query= SwissProt::P00943
         (253 letters)



>MicrobesOnline__882:207136
          Length = 251

 Score =  194 bits (493), Expect = 1e-54
 Identities = 113/253 (44%), Positives = 154/253 (60%), Gaps = 9/253 (3%)

Query: 3   KPIIAGNWKMHKTLAEAV----QFVEDVKGHVPPADEVISVVCAPFLFLDRLVQA-ADGT 57
           K +IA NWKM+KT+ EA     + V  V G +P   EV+  VC PF  L  L     D  
Sbjct: 2   KKLIAANWKMYKTIDEARATGRELVSAVAGSLPADREVL--VCPPFTALHALHDTFKDVE 59

Query: 58  DLKIGAQTMHFADQGAYTGEVSPVMLKDLGVTYVILGHSERRQMFAETDETVNKKVLAAF 117
              IG Q ++ A +GAYTGE++P ML D G  +V+ GHSERR +  E DETV +K   + 
Sbjct: 60  GFAIGGQDVYPATEGAYTGEIAPGMLLDAGCGWVLTGHSERRHILGEDDETVARKTAFSL 119

Query: 118 TRGLIPIICCGESLEEREAGQTNAVVASQVEKALAGLTPEQVKQA-VIAYEPIWAIGTGK 176
             GL  ++C GE L+EREAG+   V+A Q++  LA +    V Q+ V+AYEP+WAIGTGK
Sbjct: 120 KAGLRVVLCIGEKLDEREAGRLEDVLAHQLQVGLADVDATYVPQSLVVAYEPVWAIGTGK 179

Query: 177 SSTPEDANSVCGHIRSVVSRLFGPEAAEAIRIQYGGSVKPDNIRDFLAQQQIDGPLVGGA 236
            + P +       +RS++   +G + A AIRI YGGSVKPDN  + L+   +DG LVGGA
Sbjct: 180 VAGPAEVVEAHALVRSLLEARYGRDGA-AIRILYGGSVKPDNAAELLSLDNVDGLLVGGA 238

Query: 237 SLEPASFLQLVEA 249
           SL+  SF +++ A
Sbjct: 239 SLQAVSFSRIILA 251


Lambda     K      H
   0.318    0.134    0.389 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 197
Number of extensions: 10
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 253
Length of database: 251
Length adjustment: 24
Effective length of query: 229
Effective length of database: 227
Effective search space:    51983
Effective search space used:    51983
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate 207136 DVU1677 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00419.hmm
# target sequence database:        /tmp/gapView.856.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    4.8e-50  156.5   0.0    5.5e-50  156.3   0.0    1.0  1  lcl|MicrobesOnline__882:207136  DVU1677 triosephosphate isomeras


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207136  DVU1677 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.3   0.0   5.5e-50   5.5e-50       1     227 [.       4     242 ..       4     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: 156.3 bits;  conditional E-value: 5.5e-50
                       TIGR00419   1 lviinfKlnesvgkvelevaklaeevas..eagvevavappfvdldvvkdeve..seiqvaAqnvdavksGaftGeisA 75 
                                     l+  n+K+  ++ +      +l   va+  +a+ ev v ppf  l+ ++d  +      ++ q+v   + Ga+tGei  
  lcl|MicrobesOnline__882:207136   4 LIAANWKMYKTIDEARATGRELVSAVAGslPADREVLVCPPFTALHALHDTFKdvEGFAIGGQDVYPATEGAYTGEIAP 82 
                                     6889***988999988888888888887335899***************998854578999****************** PP

                       TIGR00419  76 emlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa.aA....... 146
                                      ml d+G+ +vl gHsErR +l e de ++ k a   + gl++v+C+ge l+erea+r  +++a++ ++  A       
  lcl|MicrobesOnline__882:207136  83 GMLLDAGCGWVLTGHSERRHILGEDDETVARKTAFSLKAGLRVVLCIGEKLDEREAGRLEDVLAHQLQVgLAdvdatyv 161
                                     *********************************************************9999998886652346777755 PP

                       TIGR00419 147 lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavl 225
                                      ++ vvA+EPv++iGtGk++ +Ae  + ++ vr  l+         +r+lyG+sv+  ++ael    +vdG+L+++a+l
  lcl|MicrobesOnline__882:207136 162 PQSLVVAYEPVWAIGTGKVAGPAEVVEAHALVRSLLEARYGRDGAAIRILYGGSVKPDNAAELLSLDNVDGLLVGGASL 240
                                     56779****************************9999988888999******************999***********9 PP

                       TIGR00419 226 ka 227
                                     +a
  lcl|MicrobesOnline__882:207136 241 QA 242
                                     87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (251 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 6.48
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory